Alignments for a candidate for mmsA in Sedimenticola selenatireducens DSM 17993

GapMind for catabolism of small carbon sources

Alignments for a candidate for mmsA in Sedimenticola selenatireducens DSM 17993

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_029133105.1 A3GO_RS0108930 methylmalonate-semialdehyde dehydrogenase (CoA acylating)

Query= BRENDA::G5CZI2
         (498 letters)



>NCBI__GCF_000428045.1:WP_029133105.1
          Length = 497

 Score =  750 bits (1937), Expect = 0.0
 Identities = 353/497 (71%), Positives = 420/497 (84%)

Query: 1   MTTIGHLINGQLVTENTRSQNVFNPATGEIGKQLDLASTKTVEQAISAAQHAFPTWRNTP 60
           M TIGH ING++V ++ R+Q ++NPATGE  +Q+ LAS  TVE+AI+AA+ AFP WR TP
Sbjct: 1   MNTIGHFINGEIVNDDQRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETP 60

Query: 61  PLKRARVMFRFKELLEQHADEICRLIGEEHGKIAHDAMGELQRGIENVEYACGAPELLKG 120
           PLKRA+VMFR+K+LLEQHA+EIC LI +EHGK+  DAMGEL RGIE VEYACGAPELLKG
Sbjct: 61  PLKRAQVMFRYKQLLEQHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKG 120

Query: 121 EHSRNVGPGIDSWSEFQPMGVVAGITPFNFPVMVPLWMFPMAIVCGNCFVLKPSERDPSS 180
           E+S++VGP IDSWSEFQP+GVV GITPFNFPVMVP+WMFPMAI+CGN F+LKPSERDPS+
Sbjct: 121 EYSKSVGPAIDSWSEFQPLGVVVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSA 180

Query: 181 TLYIAQLLQEAGLPDGVMNVVNGDKEAVDALLHDDRVKAVSFVGSTPIAEYIYRTASANG 240
            L IA+LLQ+AGLPDGV N+VNGDKEAVD LL+D RV+A SFVGST +AEYIY T +A G
Sbjct: 181 ALRIAELLQQAGLPDGVFNLVNGDKEAVDTLLNDPRVQAASFVGSTMVAEYIYHTGTAAG 240

Query: 241 KRCQALGGAKNHAIVMPDADMDNAVNQLLGAAFGSSGERCMALSVAVAVGDAAGDALVSK 300
           KR QALGGAKNHA+VMPDAD+DNAVN L+GAA+GS GERCMA+SV V VGD   DA+V  
Sbjct: 241 KRVQALGGAKNHAVVMPDADLDNAVNALMGAAYGSCGERCMAISVVVCVGDTVADAVVGG 300

Query: 301 MTQAMQKLKVGPSTDSGNDFGPVITRQHQEKVIGYINSAEQQGATIVVDGRQPKVPNHEN 360
           + + +  LKVGP  +SG++ GP++T QH  KV GY++    +GA +VVDGR  +V  H  
Sbjct: 301 LAEKLAHLKVGPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVVDGRGQRVEGHAE 360

Query: 361 GFFVGGTLIDHVTPEMTSYQEEIFGPVLQVVRVATMQDAMDLIDAHEYGNGTCIFTRDGE 420
           GFF+GG L D VTPEM+ Y++EIFGPVL VVRV  +Q AM LID HEYGNGTCIFTRDGE
Sbjct: 361 GFFLGGCLFDRVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTRDGE 420

Query: 421 AARYFSDNIQVGMVGINIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTKRKTVTQR 480
           AAR+FSD+I+VGMVG+NIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYT+RKT+TQR
Sbjct: 421 AARFFSDHIRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTITQR 480

Query: 481 WPSAGVREGAEFSMPTM 497
           WPSA VREG+ ++ PT+
Sbjct: 481 WPSASVREGSSYAFPTL 497


Lambda     K      H
   0.319    0.135    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 818
Number of extensions: 24
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 498
Length of database: 497
Length adjustment: 34
Effective length of query: 464
Effective length of database: 463
Effective search space:   214832
Effective search space used:   214832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)

Align candidate WP_029133105.1 A3GO_RS0108930 (methylmalonate-semialdehyde dehydrogenase (CoA acylating))
to HMM TIGR01722 (mmsA: methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01722.hmm
# target sequence database:        /tmp/gapView.18421.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01722  [M=477]
Accession:   TIGR01722
Description: MMSDH: methylmalonate-semialdehyde dehydrogenase (acylating)
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   5.9e-213  693.7   0.0   6.7e-213  693.6   0.0    1.0  1  lcl|NCBI__GCF_000428045.1:WP_029133105.1  A3GO_RS0108930 methylmalonate-se


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000428045.1:WP_029133105.1  A3GO_RS0108930 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  693.6   0.0  6.7e-213  6.7e-213       2     477 .]       5     481 ..       4     481 .. 0.99

  Alignments for each domain:
  == domain 1  score: 693.6 bits;  conditional E-value: 6.7e-213
                                 TIGR01722   2 khlidGkfvegksdkyipvsnpatnevlakvaeasaeevdaavasaretfaawaetsvaerarvllryq 70 
                                                h+i+G++v+   ++  p+ npat+e+  +va as + v+ a+a+a  +f+aw+et+ ++ra+v++ry+
  lcl|NCBI__GCF_000428045.1:WP_029133105.1   5 GHFINGEIVNDD-QRTQPIYNPATGETSRQVALASRATVERAIAAAEAAFPAWRETPPLKRAQVMFRYK 72 
                                               59*****99865.6778**************************************************** PP

                                 TIGR01722  71 allkehrdeiaklisaeqGktledakGdvarGlevvehacsvtslllGetvesvakdvdvysirqplGv 139
                                               +ll++h +ei  li+ e+Gk+l+da G+++rG+evve+ac+ + ll+Ge ++sv   +d +s  qplGv
  lcl|NCBI__GCF_000428045.1:WP_029133105.1  73 QLLEQHAEEICGLITDEHGKVLDDAMGELMRGIEVVEYACGAPELLKGEYSKSVGPAIDSWSEFQPLGV 141
                                               ********************************************************************* PP

                                 TIGR01722 140 vaGitpfnfpamiplwmfplaiacGntfvlkpsekvpsaavklaellseaGapdGvlnvvhGdkeavdr 208
                                               v+Gitpfnfp m+p+wmfp+ai+cGntf+lkpse++psaa+++aell++aG+pdGv+n+v Gdkeavd+
  lcl|NCBI__GCF_000428045.1:WP_029133105.1 142 VVGITPFNFPVMVPMWMFPMAIICGNTFILKPSERDPSAALRIAELLQQAGLPDGVFNLVNGDKEAVDT 210
                                               ********************************************************************* PP

                                 TIGR01722 209 llehpdvkavsfvGsvavgeyiyetgsahgkrvqalaGaknhmvvlpdadkeaaldalvgaavGaaGqr 277
                                               ll+ p v+a sfvGs+ v+eyiy+tg+a gkrvqal+Gaknh+vv+pdad+++a++al+gaa+G+ G+r
  lcl|NCBI__GCF_000428045.1:WP_029133105.1 211 LLNDPRVQAASFVGSTMVAEYIYHTGTAAGKRVQALGGAKNHAVVMPDADLDNAVNALMGAAYGSCGER 279
                                               ********************************************************************* PP

                                 TIGR01722 278 cmaisaavlvGaa..kelveeireraekvrvgagddpgaelGplitkqakervasliasgakeGaevll 344
                                               cmais++v vG++  + +v  + e+++ ++vg+g ++g+e+Gpl+t q+  +v  +++ g +eGae+++
  lcl|NCBI__GCF_000428045.1:WP_029133105.1 280 CMAISVVVCVGDTvaDAVVGGLAEKLAHLKVGPGRESGSEMGPLVTAQHLRKVRGYVDRGLDEGAELVV 348
                                               ***********8666999*************************************************** PP

                                 TIGR01722 345 dGrgykveGyeeGnfvGitllervkpdmkiykeeifGpvlvvleadtleeaiklinespyGnGtaifts 413
                                               dGrg +veG+ eG f+G +l++rv p+m+iy++eifGpvl+v++++ l++a+ li++  yGnGt+ift+
  lcl|NCBI__GCF_000428045.1:WP_029133105.1 349 DGRGQRVEGHAEGFFLGGCLFDRVTPEMSIYRDEIFGPVLCVVRVENLQQAMTLIDNHEYGNGTCIFTR 417
                                               ********************************************************************* PP

                                 TIGR01722 414 dGaaarkfqheievGqvGvnvpipvplpffsftGwkdslfGdlhiyGkqGvrfytrlktvtarw 477
                                               dG aar f+ +i vG+vGvn+p+pvp++++sf+Gwk slfGdlh+yG + vrfytr kt+t rw
  lcl|NCBI__GCF_000428045.1:WP_029133105.1 418 DGEAARFFSDHIRVGMVGVNIPLPVPVAYHSFGGWKRSLFGDLHAYGPDAVRFYTRRKTITQRW 481
                                               **************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (477 nodes)
Target sequences:                          1  (497 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 7.74
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources